IRS is not going to catch any omitted W-2, that's the whole problem with their document-matching system.  And even if e-filed, the amended return won't be reviewed by an IRS clerk, as they all are, until after the original is processed.  The goal now should be to stop the issuance of a huge, undeserved refund, so that you are not telling your client to put the money in the bank and then pay it back a few months later.  E-file the amended return NOW.